List of research methods in biology

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Template:TopicTOC-Biology This list of research methods in biology is an index to articles about research methodologies used in various branches of biology.

## Contents

* 1 Research design and analysis
* 1.1 Research designs
* 1.2 Charts and diagrams
* 1.3 Statistical analyses
* 2 Laboratory techniques
* 3 Field techniques
* 4 Computational tools
* 4.1 Mathematical models
* 4.2 Algorithms
* 5 References
* 6 External links

## Research design and analysis

### Research designs

Research design | Utility | Potential analysis

|
|

Between-group design | Experiment that has two or more groups of subjects each being tested by a different testing factor simultaneously | Student's t-test, Analysis of variance, Mann–Whitney U test
Repeated measures design | A research design that involves multiple measures of the same variable taken on the same or matched subjects either under different conditions or over two or more time periods.[1] | Paired t-test, Wilcoxon signed-rank test

### Charts and diagrams

Analysis | Utility | Branch

|
|

Dose–response curves | Graph that shows the magnitude of the response of an organism, as a function of exposure (or doses) to a stimulus or stressor (usually a chemical) after a certain exposure time[2] | Physiology
Electroencephalogram | Graph that shows voltage fluctuations resulting from ionic current within the neurons of the brain[3] | Neuroscience
Electrocardiogram | Graph of voltage versus time of the electrical activity of the heart[4] using electrodes placed on the skin | Physiology
Identification key | Used to identify a specimen organism from a set of known taxa.[5] | Systematics,

Taxonomy

Manhattan plot | Used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values. The plot is commonly used in genome-wide association studies (GWAS) to display significant SNPs.[6] | Genetics
Pedigree chart | Used to show the occurrence of phenotypes of a particular gene or organism and its ancestors from one generation to the next,[7][8][9] most commonly humans, show dogs,[10] and race horses | Genetics
Phylogenetic tree | Used to show the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics | Systematics, Evolutionary biology
Population pyramid | Used to illustrate the distribution of a population (typically that of a country or region of the world) by age groups and sex; it typically forms the shape of a pyramid when the population is growing[11] | Population ecology
Punnett square | Used to predict the genotypes of a particular cross or breeding experiment | Genetics

### Statistical analyses

Analysis | Utility | Type

|
|

Analysis of variance | A collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means | Statistical model
Chi-squared test | A statistical hypothesis test that is valid to perform when the test statistic is chi-squared distributed under the null hypothesis, specifically Pearson's chi-squared test and variants thereof | Statistical hypothesis test
Mann–Whitney U test | A statistical hypothesis test of the null hypothesis that, for randomly selected values X and Y from two populations, the probability of X being greater than Y is equal to the probability of Y being greater than X | Nonparametric statistics
Student's t-test | Any statistical hypothesis test in which the test statistic follows a Student's t-distribution under the null hypothesis | Parametric statistics

## Laboratory techniques

Method | Utility | Branches

|
|

Agarose gel electrophoresis | Used to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar | Biochemistry, Molecular biology, Genetics
Animal Model | Used for researching diseases and disorders in humans. Some animals may have human-like traits, such as mice, while others may have traits that are ideal for research, such as the squid giant axon | Biochemistry, Neuroscience, Physiology
Biological ablation | Used to remove a biological structure or functionality | Genetics, Physiology
Calcium imaging | Used to optically measure the status of calcium ions (Ca2+) in an isolated cell, tissue or medium | Physiology
Cell isolation | Process of separating individual living cells from a solid block of tissue or cell suspension | Cell biology
Centrifugation | Use of centrifugal force to separate particles from a solution according to their size, shape, density, medium viscosity, and rotor speed | Cell biology, Biochemistry
CRISPR gene editing | Used to modify the genomes of living organisms based on a simplified version of the bacterial CRISPR-Cas9 antiviral defense system | Molecular biology
DNA sequencer | Used to automate the DNA sequencing process | Genetics, Molecular biology
Enzyme-linked immunosorbent assay (ELISA) | Used to detect the presence of a ligand (commonly a protein) in a liquid sample using antibodies directed against the protein to be measure | Biochemistry, Molecular biology
Gene knockout | Used to make one of an organism's genes inoperative ("knocked out" of the organism) | Molecular biology, Genetics
Immunostaining | Used of an antibody-based method to detect a specific protein in a sample | Molecular biology, Biochemistry
Intracellular recording | Used to measure the voltage across a cell membrane | Neuroscience, Electrophysiology
Microarray | Assays (tests) large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods | Genetics, Molecular biology
Microelectrode array | Devices that contain multiple (tens to thousands) microelectrodes through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry | Neuroscience
Microscope | Used to examine objects that are too small to be seen by the naked eye | Cell biology
Molecular cloning | Used to assemble recombinant DNA molecules and to direct their replication within host organisms.[12] | Molecular biology
Northern blot | Used to study gene expression by detection of RNA (or isolated mRNA) in a sample.[13][14] | Molecular biology
Optogenetics | Uses light to control neurons that have been genetically modified to express light-sensitive ion channels | Neuroscience
Oscilloscope | Used to graphically displays varying signal voltages, usually as a calibrated two-dimensional plot of one or more signals as a function of time | Neuroscience, Physiology
Paper chromatography | Used to separate coloured chemicals or substances.[15] | Molecular biology
Patch clamp | Used to study ionic currents in individual isolated living cells, tissue sections, or patches of cell membrane | Electrophysiology, Neuroscience
Polymerase chain reaction (PCR) | Used to rapidly make millions to billions of copies (complete copies or partial copies) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail | Genetics, Molecular biology
Somatic cell nuclear transfer | Used for creating a viable embryo from a body cell and an egg cell | Developmental biology
Southern blot | Used to detect specific DNA sequence in DNA samples | Molecular biology
Test cross | Used to determine whether an individual is homozygous or heterozygous dominant | Genetics
Voltage clamp | Used to measure the ion currents through the membranes of excitable cells, such as neurons, while holding the membrane voltage at a set level.[16] | Physiology, Neuroscience
Western blot | Used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract | Molecular biology
X-ray crystallography | Used to determine the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions | Structural biology

## Field techniques

Method | Utility | Branches

|
|

Distance sampling | Used for estimating the density and/or abundance of populations | Ecology
Mark and recapture | Used to estimate an animal population's size where it is impractical to count every individual.[17] | Ecology

## Computational tools

### Mathematical models

Model | Utility | Branches

|
|

Exponential integrate-and-fire | Describes compact and computationally efficient nonlinear spiking neuron models with one or two variables | Neuroscience
FitzHugh–Nagumo model | Describes a prototype of an excitable system (e.g., a neuron) | Neuroscience
Hardy–Weinberg principle | States that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences | Genetics, Evolutionary biology
Hodgkin–Huxley model | Describes how action potentials in neurons are initiated and propagated | Neuroscience
Infinite sites model | Allows for the calculation of heterozygosity, or genetic diversity, in a finite population and for the estimation of genetic distances between populations of interest[18] | Evolutionary biology
Logistic growth | Describes the growth of a population as exponential, followed by a decrease in growth, and bound by a carrying capacity due to environmental pressures.[19] | Ecology
Lotka–Volterra equations | Describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey | Ecology
Moran process | Stochastic process that describes finite populations | Genetics
Species–area relationship | describes the relationship between the area of a habitat, or of part of a habitat, and the number of species found within that area | Ecology

### Algorithms

Algorithm | Utility | Branches

|
|

Evolutionary algorithm | Uses mechanisms inspired by biological evolution. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions. | Neuroscience

## References

1. ↑ Salkind, Neil J. (2010). Repeated Measures Design. SAGE. doi:10.4135/9781412961288. ISBN 9781412961271. http://methods.sagepub.com/reference/encyc-of-research-design/n378.xml. Retrieved 8 January 2019.
2. ↑ Crump, K. S.; Hoel, D. G.; Langley, C. H.; Peto, R. (1 September 1976). "Fundamental Carcinogenic Processes and Their Implications for Low Dose Risk Assessment". Cancer Research 36 (9 Part 1): 2973–2979. PMID 975067. http://cancerres.aacrjournals.org/content/36/9_Part_1/2973.long. Retrieved 16 March 2024.
3. ↑ Niedermeyer E.; da Silva F.L. (2004). Electroencephalography: Basic Principles, Clinical Applications, and Related Fields. Lippincott Williams & Wilkins. ISBN 978-0-7817-5126-1.
4. ↑ Lilly, Leonard S, ed (2016). Pathophysiology of Heart Disease: A Collaborative Project of Medical Students and Faculty (sixth ed.). Lippincott Williams & Wilkins. p. 74. ISBN 978-1451192759.
5. ↑ Winston, Judith E. (1999). "Keys". Describing species: practical taxonomic procedure for biologists. New York: Columbia University Press. pp. 367–381. ISBN 978-0-231-06824-6.
6. ↑ Gibson, Greg (2010). "Hints of hidden heritability in GWAS". Nature Genetics 42 (7): 558–560. doi:10.1038/ng0710-558. PMID 20581876. Bibcode: 2010NaGen..42..558G.
7. ↑ pedigree chart Genealogy Glossary - About.com, a part of The New York Times Company.
8. ↑ "HELP - Ancestral File - Pedigree Chart". http://www.familysearch.org/eng/helps/Search/Ancestors/afpedigree.htm.
9. ↑ Documenting Your Pedigree Chart By Melody Daisson - GeneaSearch.com
10. ↑ "AKC Pedigree: How to Purchase a Document on Your Dog's Lineage". http://www.akc.org/reg/pedigree_overview.cfm.
11. ↑ "Population Pyramids of the World from 1950 to 2100". http://populationpyramid.net/.
12. ↑ Watson, James D. (2007). Recombinant DNA: genes and genomes: a short course. San Francisco: W.H. Freeman. ISBN 978-0-7167-2866-5.
13. ↑ Alberts, B., Johnson, A., Lewis, J. Raff, M., Roberts, K., Walter, P. 2008. Molecular Biology of the Cell, 5th ed. Garland Science, Taylor & Francis Group, NY, pp 538–539.
14. ↑ Kevil, C. G., Walsh, L., Laroux, F. S., Kalogeris, T., Grisham, M. B., Alexander, J. S. (1997) An Improved, Rapid Northern Protocol. Biochem. and Biophys. Research Comm. 238:277–279.
15. ↑ "Paper chromatography | chemistry" (in en). Encyclopedia Britannica. https://www.britannica.com/science/paper-chromatography.
16. ↑ Nowotny, Dr Thomas; Levi, Dr Rafael (2014). "Voltage-Clamp Technique". in Jaeger, Dieter (in en). Encyclopedia of Computational Neuroscience. Springer New York. pp. 1–5. doi:10.1007/978-1-4614-7320-6_137-2. ISBN 9781461473206.
17. ↑ "Mark-Recapture". http://www2.nau.edu/lrm22/lessons/mark_recapture/mark_recapture.html.
18. ↑ Kimura, Motoo (1969-04-01). "The Number of Heterozygous Nucleotide Sites Maintained in a Finite Population Due to Steady Flux of Mutations". Genetics 61 (4): 893–903. doi:10.1093/genetics/61.4.893. ISSN 0016-6731. PMID 5364968.
19. ↑ Renshaw, Eric (1991). Modeling Biological Populations in Space and Time. Cambridge University Press. pp. 6–9.

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